Mixed model approaches for the identification of QTLs within a maize hybrid breeding program

Two outlines for mixed model based approaches to quantitative trait locus (QTL) mapping in existing maize hybrid selection programs are presented: a restricted maximum likelihood (REML) and a Bayesian Markov Chain Monte Carlo (MCMC) approach. The methods use the in-silico-mapping procedure developed by Parisseaux and Bernardo (2004) as a starting point. The original single-point approach is extended to a multi-point approach that facilitates interval mapping procedures. For computational and conceptual reasons, we partition the full set of relationships from founders to parents of hybrids into two types of relations by defining so-called intermediate founders. QTL effects are defined in terms of those intermediate founders. Marker based identity by descent relationships between intermediate founders define structuring matrices for the QTL effects that change along the genome. The dimension of the vector of QTL effects is reduced by the fact that there are fewer intermediate founders than parents. Furthermore, additional reduction in the number of QTL effects follows from the identification of founder groups by various algorithms. As a result, we obtain a powerful mixed model based statistical framework to identify QTLs in genetic backgrounds relevant to the elite germplasm of a commercial breeding program. The identification of such QTLs will provide the foundation for effective marker assisted and genome wide selection strategies. Analyses of an example data set show that QTLs are primarily identified in different heterotic groups and point to complementation of additive QTL effects as an important factor in hybrid performance

Qubit-flip-induced cavity mode squeezing in the strong dispersive regime of the quantum Rabi model

Squeezed states of light are a set of nonclassical states in which the quantum fluctuations of one quadrature component are reduced below the standard quantum limit. With less noise than the best stabilised laser sources, squeezed light is a key resource in the field of quantum technologies and has already improved sensing capabilities in areas ranging from gravitational wave detection to biomedical applications. In this work we propose a novel technique for generating squeezed states of a confined light field strongly coupled to a two-level system, or qubit, in the dispersive regime. Utilising the dispersive energy shift caused by the interaction, control of the qubit state produces a time-dependent change in the frequency of the light field. An appropriately timed sequence of sudden frequency changes reduces the quantum noise fluctuations in one quadrature of the field well below the standard quantum limit. The degree of squeezing and the time of generation are directly controlled by the number of frequency shifts applied. Even in the presence of realistic noise and imperfections, our protocol promises to be capable of generating a useful degree of squeezing with present experimental capabilities

The heterogeneity of wooded-agricultural landscape mosaics influences woodland bird community assemblages

Context Landscape heterogeneity (the composition and configuration of different landcover types) plays a key role in shaping woodland bird assemblages in wooded-agricultural mosaics. Understanding how species respond to landscape factors could contribute to preventing further decline of woodland bird populations. Objective To investigate how woodland birds with different species traits respond to landscape heterogeneity, and to identify whether specific landcover types are important for maintaining diverse populations in wooded-agricultural environments. Methods Birds were sampled from woodlands in 58 2 x 2 km tetrads across southern Britain. Landscape heterogeneity was quantified for each tetrad. Bird assemblage response was determined using redundancy analysis combined with variation partitioning and response trait analyses. Results For woodland bird assemblages, the independent explanatory importance of landscape composition and landscape configuration variables were closely interrelated. When considered simultaneously during variation partitioning, the community response was better represented by compositional variables. Different species responded to different landscape features and this could be explained by traits relating to woodland association, foraging strata and nest location. Ubiquitous, generalist species, many of which were hole-nesters or ground foragers, correlated positively with urban landcover while specialists of broadleaved woodland avoided landscapes containing urban areas. Species typical of coniferous woodland correlated with large conifer plantations. Conclusions At the 2 x 2 km scale, there was evidence that the availability of resources provided by proximate landcover types was highly important for shaping woodland bird assemblages. Further research to disentangle the effects of composition and configuration at different spatial scales is advocated

The influence of the landscape structure within buffer zones, catchment land use and instream environmental variables on mollusc communities in a medium-sized lowland river

The world’s freshwater molluscan fauna is facing unprecedented threats from habitat loss and degradation. Declines in native populations are mostly attributed to the human impact, which results in reduced water quality. The objectives of our survey were to analyse the structure of the mollusc communities in a medium-sized lowland river and to determine the most important environmental variables at different spatial scales, including landscape structure, catchment land use and instream environmental factors that influence their structure. Our survey showed that a medium-sized river, that flows through areas included in the European Ecological Natura 2000 Network Programme of protected sites, provides diverse instream habitats and niches that support 47 mollusc species including Unio crassus, a bivalve of Community interest, whose conservation requires the designation of a special conservation area under the Habitats Directive Natura 2000. This survey showed that mollusc communities are impacted by several environmental variables that act together at multiple scales. The landscape structure within buffer zones, catchment land use and instream environmental variables were all important and influenced the structure of mollusc communities. Therefore, they should all be taken into consideration in the future restoration of the river, future management projects and programmes for the conservation of biodiversity in running waters. The results of this study may be directly applicable for the rehabilitation of river ecosystems and are recommended to stakeholders in their future decision concerning landscape planning, monitoring species and their habitats, conservation plans and management in accordance with the requirements of sustainable development